In the mean time the Eparchy of Tiruvalla was blessed with an Auxiliary Bishop in the person of Most Rev. Dr. Thomas Mar Koorilos. He was consecrated Bishop by His Excellency Geevarghese Mar Timotheos on 17th July 1997 at St. John's Cathedral, Tiruvalla.

With the appointment of Rev. Dr. John Berchmans OIC on Dec 26th, 1997 as the Co-Ordinator of the Malankara Catholic Communities in the Extra-territorial regions in India by the Metropolitan Archbishop of the Syro-Malankara Catholic Church, the ecciesial life of these parish communities was coordinated.

Most Rev. Yoohanon Mar Chrysostom was consecrated as Bishop of Marthandom and Joshua Mar Ignathios as the Auxiliary Bishop of the Metropolitan Eparchy of Trivandrum by Archbishop Cyril Mar Baselios at Mar Ivanios Stadium, Nalanchira on 29th June 1998. Most Rev. Yoohanon Mar Chrysostom on 1st July 1998 at Christuraja Cathedral by His Grace Cyril Mar Baselios.

His Excellency Paulos Mar Philoxenos passed away on 3rd Nov 1998 and was entombed at St. John's Cathedral, Tiruvalla.

The Syro-Malankara Catholic Church celebrated the Great Jubilee 2000 in Rome on 19th -21st Nov 2000. Holy Father Pope John Paul II in an audience with the Hierarchy and the representatives of the Clergy, the Religious and Laity of the Syro-Malankara Catholic Church said, "Seventy years ago, Metropolitan Archbishop Mar Ivanios, Bishop Mar Theophilos and their companions entered into full communion with the See of Peter, because they were profoundly convinced of the truth of the words found beneath the dome of the Vatican Basilica: Hinc una fides mundo reflget. 'From here the one faith shines forth in the world'. They understood that 'the Church is one, the Church of Christ between East and West' (Orientale Lumen, 20); and they knew that, in entering the communion of the Catholic Church, they 'did not at all intend to deny their fidelity to their own tradition' (ibid., 21). In the years since their decision, God has abundantly blessed the Syro-Malankara Church in her work for Christian unity."

A Great Jubliee Conference was organized by the Syro-Malankara Catholic Church in the Pope John Paul II auditorium of the Pontifical Urbanian University, Rome on Nov 20th, 2000. His Eminence Achille Cardinal Silvestrini, Prefect of the Congregation for Oriental Churches presided over the Conference. His Eminence Roger Cardinal Marie Elie Etchegaray, the President of the Central Committee for the Great Jubliee, His Eminence Crescenzio Cardinal Sepe, the Prefect of the Congregation for the Evangelisation of Peoples, His Eminence Simon Cardinal Lourdusamy, Perfect Emeritus of the Congregation for the Oriental Churches and His Grace Metropolitan Archbishop Cyril Mar Baselios spoke on the occasion.

The Holy Qurbono in Malankara-Syro Antiochene rite was celebrated on November 21, 2000, at the Basilica of Santa Maria in Trastevere in Rome, presided by His Beatitude Ignace Moussa I Daoud, Patriarch of the Syro Antiochean Catholics and His Grace Cyril Mar Baselios, Metropolitan Archbishop of the Syro-Malankara Catholic Church. The dignitaries present at the Holy Mass were His Eminence Achille Cardinal Silvestrini, Perfect of the Congregation for the Oriental Churches, His Grace Archbishop Stefan Miroslav Marusyn, Secretary of the Congregation for the Oriental Churches, His Excellency Bishop Emile Eid, Procurator in Rome of the Antiochean Catholics in Latin America and Prof. Andrea Riccardi, the Founder of Sant'Egidio Community.

Christu Jayanthi Maha Jubilee (Great Jubilee of the Birth of our Lord Jesus Christ) and the Sapthathy of the Re-union Movement of the Syro-Malankara Catholic Church were celebrated jointly at Tiruvalla on 26, 27 and 28 December 2000. His Beatitude Ignace Moussa Daoud, the Perfect of the Congregation for the Oriental Churches was the Chief Guest for the Celebration.

In response to the request of the Syro-Malankara Catholic Faithful in Doha and Dubai, the Major Archbishop-Catholicos appointed residedent priests in those countries for the pastoral care.

A significant development in this period has been the establishment of parishes for the faithful of the Syro-Malankara Catholic Church in the United States of America. The Holy Father Paul II appointed Rt. Rev. Msgr. Isaac Thottunkal, the Proto Syncellus of Bathery, as Apostolic Visitor for the Syro-Malankarites residing in North America and Europe and the Auxiliary Bishop of Trivandrum on 18 June 2001. he was ordained as Bishop by Metropolitan Archbishop Cyril Mar Baselios at Mar Ivanios Nagar, Tirumoolapuram, Tiruvalla with the name Isaac Mar Cleemis on 15 August 2001. His Excellency Isaac Mar Cleemis started his Episcopal Ministry in North America residing at various American Rectories. By the providence of God the Church could acquire a house in Hillside Avenue, New York in 2012. The house was named as Mar Ivanios Malankara Catholic Centre. It is being used as the office of the Apostolic Visitor and the headquarters of North American ecciesial activities of the Syro-Malankara Catholic Church.

Upon the request of His Excellency Geevarghese Mar Timotheos the Holy See established the Eparchy of Muvattupuzha, bifurcating the Eparchy of Tiruvalla, on